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- PDB-1pib: Solution structure of DNA containing CPD opposited by GA -

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Basic information

Entry
Database: PDB / ID: 1pib
TitleSolution structure of DNA containing CPD opposited by GA
Components
  • 5'-D(*CP*GP*CP*AP*TP*TP*AP*CP*GP*C)-3'
  • 5'-D(*GP*CP*GP*TP*GP*AP*TP*GP*CP*G)-3'
KeywordsDNA / Cis-syn Cyclobutane Pyrimidine Dimer / CPD containing DNA / helical distortion / Thyminedimer
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsLee, J.H. / Park, C.J. / Shin, J.S. / Choi, B.S.
CitationJournal: Nucleic Acids Res. / Year: 2004
Title: NMR structure of the DNA decamer duplex containing double T*G mismatches of cis-syn cyclobutane pyrimidine dimer: implications for DNA damage recognition by the XPC-hHR23B complex.
Authors: Lee, J.H. / Park, C.J. / Shin, J.S. / Ikegami, T. / Akutsu, H. / Choi, B.S.
History
DepositionMay 30, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*CP*GP*CP*AP*TP*TP*AP*CP*GP*C)-3'
B: 5'-D(*GP*CP*GP*TP*GP*AP*TP*GP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,1062
Polymers6,1062
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 50structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: DNA chain 5'-D(*CP*GP*CP*AP*TP*TP*AP*CP*GP*C)-3'


Mass: 3004.981 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*CP*GP*TP*GP*AP*TP*GP*CP*G)-3'


Mass: 3101.028 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
3322D NOESY
342DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM DNA, 20mM phosphate buffer90% H2O/10% D2O
21mM DNA, 20mM phosphate buffer99.9% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mM NaCl 7.0 ambient 277 K
2100mM NaCl 7.0 ambient 300 K
3100mM NaCl 7.0 ambient 290 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeFrank Delaglioprocessing
X-PLOR3.1Brungerstructure solution
Sparky3.106T. D. Goddarddata analysis
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 50 / Conformers submitted total number: 16

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